It probably falls in because I think the majority of apple still thinks users will choose an autosync, so cleaning up iTunes would therefore clean up the iPod.

It is not as an elegant solution, but if you are on manual update you could select the iPod, sort by song title, and just scroll down looking for duplicates you want to bump off. Would take longer than the other, but could work.

I agree,
In manual mode we should be able to use the "search duplicate songs" function. I prefer not to have all my songs on my computer, but rather keep them solely on my ipod. Therefore I would just like to delete the songs on it.